Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00911.N25
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11062
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:7696 original size:45 final size:45
Alignment explanation
Indices: 7627--7712 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
7617 CGGTATCTGC
* * *
7627 TATCTTTGATTTGCTCCCTATCTAATACAGAGACGCCAAATCTAT
1 TATCTTCGATCTGCTCCCCATCTAATACAGAGACGCCAAATCTAT
*
7672 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAAT
1 TATCTTCGATCTGCTCCCCATCTAATACAGAGACGCCAAAT
7713 TTGCTTCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCATCTAATACAGAGACGCCAAATCTAT
Found at i:8167 original size:87 final size:87
Alignment explanation
Indices: 7898--8168 Score: 241
Period size: 87 Copynumber: 3.1 Consensus size: 87
7888 AGGCCAAATT
* * *
7898 TGCTATGCCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTGCTTCAGT
1 TGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGT
*
7963 ATAAACATCTGAAGGTTAGATC
66 AAAAACATCTGAAGGTTAGATC
* * * * * ** * *
7985 TGTTATG---T-G-TCTGCT-CTCCGTCGAATA-TGGAGACGCCAGATCTGTTATCTTGGATCTG
1 TGCTATGTCTTCGATTTGCTCCT-TGT-AAACACAAGA-ATGCCAAATC----ATCTTGGATCTG
* * * *
8043 CTTTGATGTGAAAACATCTGAAAGTCAGATC
59 C-TTCA-GTAAAAACATCTGAAGGTTAGATC
8074 TGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGT
1 TGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGT
*
8139 AAAAACATCCGAAGGTTAGATC
66 AAAAACATCTGAAGGTTAGATC
*
8161 TACTATGT
1 TGCTATGT
8169 ATCTGCTCTC
Statistics
Matches: 137, Mismatches: 31, Indels: 32
0.69 0.16 0.16
Matches are distributed among these distances:
81 2 0.01
82 7 0.05
83 12 0.09
84 1 0.01
87 46 0.34
88 6 0.04
89 39 0.28
92 1 0.01
93 12 0.09
94 9 0.07
95 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (87 bp):
TGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGT
AAAAACATCTGAAGGTTAGATC
Found at i:8312 original size:95 final size:93
Alignment explanation
Indices: 7996--8318 Score: 280
Period size: 95 Copynumber: 3.5 Consensus size: 93
7986 GTTATGTGTC
* * *
7996 TGCTCTCCGTCGAATATGGAGACGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAAAACA-T
1 TGCTCTCCGTCGAA-ATAGAGAAGCCAAATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATT
8060 CTGAAAGTCAGATCTGCTATGTCTTCGATT
65 C-GAAAGTCAGATCTGCTATGTCTTCGATT
* * * * *
8090 TG--CTCC-TTGTAAACACAAGAATGCCAAATC----ATCTTGGATCTGC-TTCA-GTAAAAACA
1 TGCTCTCCGTCG-AAATA-GAGAA-GCCAAATCTGTTATCTTGGATCTGCTTTGATGTGAAAACA
* * * * *
8146 TCCGAAGGTTAGATCTACTATG---T--ATC
63 TTCGAAAGTCAGATCTGCTATGTCTTCGATT
** * * * *
8172 TGCTCTCCGTTTAAATATGGAGATGCCAGATCTGTTATCTAGGATCTGCTTTGATGTGAGAACAT
1 TGCTCTCCGTCGAAATA--GAGAAGCCAAATCTGTTATCTTGGATCTGCTTTGATGTGAAAACAT
8237 TCGAAAGTCAGATCTGCTATGTCTTCGATT
64 TCGAAAGTCAGATCTGCTATGTCTTCGATT
*
8267 TGCTCTCCGTCGAAGATAGAGAAGCCAAATCTTATTATCTTGGATCTGCTTT
1 TGCTCTCCGTCGAA-ATAGAGAAGCCAAATC-TGTTATCTTGGATCTGCTTT
8319 AGTGTAAACA
Statistics
Matches: 174, Mismatches: 34, Indels: 41
0.70 0.14 0.16
Matches are distributed among these distances:
82 4 0.02
84 16 0.09
85 5 0.03
87 24 0.14
88 16 0.09
89 16 0.09
90 25 0.14
91 3 0.02
92 9 0.05
93 8 0.05
94 13 0.07
95 32 0.18
96 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (93 bp):
TGCTCTCCGTCGAAATAGAGAAGCCAAATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATTC
GAAAGTCAGATCTGCTATGTCTTCGATT
Found at i:8457 original size:84 final size:84
Alignment explanation
Indices: 8358--8557 Score: 341
Period size: 84 Copynumber: 2.4 Consensus size: 84
8348 ATGCTTTGGT
*
8358 CTGTTACCCTACTGCTTAGGGGGTTAAGGCGCGAT-TTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTGTTACCCTACTGCTTAGGGGATTAAGGCGCG-TCTTCGATCTGCTCCACTACTGCTTAGGGAG
8422 ATAAGATCTGT-AAATTTAAC
65 ATAAGATCT-TCAAATTTAAC
* *
8442 CTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGTTTAGGGAGA
1 CTGTTACCCTACTGCTTAGGGGATTAAGGCGCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
8507 TAAGATCTTCAAATTTAAC
66 TAAGATCTTCAAATTTAAC
8526 CTGTTACCCTACTGCTTAGGGGATTAAGGCGC
1 CTGTTACCCTACTGCTTAGGGGATTAAGGCGC
8558 TGAATTTTGT
Statistics
Matches: 110, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
83 2 0.02
84 108 0.98
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (84 bp):
CTGTTACCCTACTGCTTAGGGGATTAAGGCGCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTTCAAATTTAAC
Found at i:8539 original size:43 final size:43
Alignment explanation
Indices: 8407--8546 Score: 127
Period size: 43 Copynumber: 3.3 Consensus size: 43
8397 ATCTGCTCCA
8407 CTACTGCTTAGGGAGATAAGATCTGT-AAATTTAACCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCT-TCAAATTTAACCTGTTACC
* *
8450 CTACTGCTTAGGG-GATTAAGGCGAGTCTTC-GA--T---CTGCT-CC
1 CTACTGCTTAGGGAGA-TAA---GA-TCTTCAAATTTAACCTGTTACC
*
8490 ACTACTGTTTAGGGAGATAAGATCTTCAAATTTAACCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTTCAAATTTAACCTGTTACC
8534 CTACTGCTTAGGG
1 CTACTGCTTAGGG
8547 GATTAAGGCG
Statistics
Matches: 76, Mismatches: 6, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
37 5 0.07
38 3 0.04
40 3 0.04
41 19 0.25
42 4 0.05
43 32 0.42
44 3 0.04
46 4 0.05
47 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (43 bp):
CTACTGCTTAGGGAGATAAGATCTTCAAATTTAACCTGTTACC
Found at i:9464 original size:7 final size:7
Alignment explanation
Indices: 9452--9513 Score: 76
Period size: 7 Copynumber: 8.9 Consensus size: 7
9442 GACCTTTCCA
9452 TTTTTTC
1 TTTTTTC
9459 TTTTTTC
1 TTTTTTC
9466 TTTTTTC
1 TTTTTTC
9473 TTTTTAT-
1 TTTTT-TC
9480 TTTTTTCC
1 TTTTTT-C
9488 TCTTTTTC
1 T-TTTTTC
9496 --TTTTC
1 TTTTTTC
9501 TTTTTTC
1 TTTTTTC
9508 TTTTTT
1 TTTTTT
9514 TTTGAAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.10
6 1 0.02
7 35 0.71
8 3 0.06
9 5 0.10
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Done.